[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

[Maryam Sadat Sadeghi]

Hi All,

I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error:

readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning: carbon radical, carbocation or carbanion not supported; skipped molecule.

How can I fix this problem? Changing the ligand IDs and names does not help. I even tried to make 2 separate mol2 files for each chain in the crystal structure, but still get the same error while converting to str file...